The overall goal of this proposal is to improve the quality, reliability, and interlaboratory comparability of peptide mass spectrometry data. Mass spectrometry (MS) has become a fundamental technology for the identification and quantitative analysis of proteins, protein interactions, and protein post-translational modifications. These analyses are an important part of solving biological problems that involve changes in protein abundance in response to disease, drug treatment, and genetic or environmental perturbations. Unfortunately, the application of protein mass spectrometry measurements in the clinical laboratory has been limited. Unlike most clinical assays by mass spectrometry, which use microflow liquid chromatography, peptide measurements are commonly performed using a nanoflow liquid chromatograph interface to the mass spectrometer (nanoflow LC-MS). Despite their analytical power, these nanoflow LC-MS methods have been difficult to apply robustly in quantitative assays involving large numbers of samples from a challenging sample matrix. The successful completion of our project will result in a peptide analysis platform that can automatically assess problems with the nanoflow LC-MS system and correct the problem during an analytical run and will significantly improve the robustness and reproducibility of peptide mass spectrometry measurements.